Currently db_ucsc
and db_ensembl
are available for connections.
Usage
db_ucsc(
dbname,
host = "genome-mysql.cse.ucsc.edu",
user = "genomep",
password = "password",
port = 3306,
...
)
db_ensembl(
dbname,
host = "ensembldb.ensembl.org",
user = "anonymous",
password = "",
port = 3306,
...
)
Examples
if (FALSE) { # \dontrun{
if (require(RMariaDB)) {
library(dplyr)
ucsc <- db_ucsc("hg38")
# fetch the `refGene` tbl
tbl(ucsc, "refGene")
# the `chromInfo` tbls have size information
tbl(ucsc, "chromInfo")
}
} # }
if (FALSE) { # \dontrun{
if (require(RMariaDB)) {
library(dplyr)
# squirrel genome
ensembl <- db_ensembl("spermophilus_tridecemlineatus_core_67_2")
tbl(ensembl, "gene")
}
} # }